diff --git a/.gitignore b/.gitignore index fa6d2d8..2e36968 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ 20* -*.cfg~ -*.log -relacsdebug* -bugs -coredumps \ No newline at end of file +*/*.cfg~ +*/*.log +*/relacsdebug* +*/bugs +*/coredumps \ No newline at end of file diff --git a/rfs/macrorfs.cfg b/rfs/macrorfs.cfg new file mode 100644 index 0000000..2318234 --- /dev/null +++ b/rfs/macrorfs.cfg @@ -0,0 +1,35 @@ +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + +$Calibrate Robot +CalibrateRobot: + +$Receptive Field low +ReceptiveField: amplitude=10mV, repeats=4 + +$Receptive Field mid +ReceptiveField: amplitude=20mV, repeats=4 + +$Receptive Field high +ReceptiveField: amplitude=40mV, repeats=4 + +$Robot to fish position +RobotToFishPosition: + +$FICurve AM +FICurve: am=true; + +$Noise AM: contrast=10% +Pause: duration=200ms +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=10%; repeats=5 +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=5%; repeats=5 +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=20% + +$Back +switch macros.cfg + + +#$SAMs AM +#SAM: deltaf=(100..300..10,alternateout,r=3)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=2; +#SAM: deltaf=(20..90..10,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=4; +#SAM: deltaf=(2..18..2,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=2s; repeats=4; diff --git a/rfs/macros.cfg b/rfs/macros.cfg new file mode 100644 index 0000000..fec4638 --- /dev/null +++ b/rfs/macros.cfg @@ -0,0 +1,51 @@ +$START startup nobutton keep +shell rm -f $RELACSDEFAULTPATH/* + +$DISKSPACE stopsession nobutton keep +message Diskspace: $(DS=$(df -B 1M . | tail -n 1 | awk '{ print $4 }'); + [ $DS -lt 1000 ] && echo "

! Warning !

Less than ${DS}MB + of free disk space left! +

Please make backups and clean up to make room for the next recording!") + + +############################################################################# +$Search fallback keep +BaselineActivity: repeats=0; isimax=20ms; isistep=0.2ms; auto=always; +SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=true; freqsel=relative to EOD; sinewave=true; +SAM: deltaf=20; contrast=20; duration=400ms; pause=100ms; repeats=0; am=false; freqsel=absolute; sinewave=true; + + +############################################################################# +$Start startsession keep overwrite +Pause: duration=0.2s; +detector: autoconfigure 0.2 +macro Baseline +detector Spikes-1: save + +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + + +############################################################################# +$AM +switch macrosam.cfg + +$Receptive fields +switch macrorfs.cfg + + +############################################################################# +$Calib direct +CalibEField: am=0; + +$Calib AM +CalibEField: am=1; + +$Check SAM +SAM: am=false; freqsel=relative to EOD; repeats=0; contrast=20%; deltaf=20Hz; + + +############################################################################# + +$Idle +Pause: duration=0; diff --git a/rfs/macrosam.cfg b/rfs/macrosam.cfg new file mode 100644 index 0000000..9ad83ef --- /dev/null +++ b/rfs/macrosam.cfg @@ -0,0 +1,38 @@ +############################################################################# +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + +$SAMs AM +SAM: deltaf=(100..300..10,alternateout,r=3)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: deltaf=(20..90..10,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: deltaf=(2..18..2,alternateout,r=2)Hz; am=true; freqsel=relative to EOD; duration=2s; repeats=4; + +$Chirps EOD +#Chirps: chirpsize=100Hz; deltaf=(-250,-240,-230,-220,-210,-200,-190,-180,-170,-160,-150,-140,-130,-120,-110,-100,-90,-80,-70,-60,-50,-40,-30,-20,-10,10,20,30,40,50,60,70,80,90,100,110,120,130,140,150,160,170,180,190,200,210,220,230,240,250); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false +Chirps: chirpsize=60Hz; deltaf=(-250,-200,-150,-100,-80,-60,-40,-20,-10,10,20,40,60,80,100,150,200,250); contrast=10%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false + +$Nervetest +Chirps: chirpsize=100Hz; deltaf=(20); contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=true; sinewave=true; playback=false + +$FICurve AM +FICurve: am=true; + +$Noise AM: contrast=10% +Pause: duration=200ms +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=10% +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=5% +FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=20% + +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn200Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn100Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn50Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast +!FileStimulus: file=/home/efish/stimuli/whitenoise/gwn25Hz10s0.3.dat; sigstdev=0.3; am=true; contrast=$contrast + + +############################################################################# +$DC +switch macrosdc.cfg + +$Back +switch macros.cfg diff --git a/rfs/macrosdc.cfg b/rfs/macrosdc.cfg new file mode 100644 index 0000000..09ec73a --- /dev/null +++ b/rfs/macrosdc.cfg @@ -0,0 +1,69 @@ +############################################################################# +$Baseline +BaselineActivity: repeats=3000; saveeodtrace=true; + +$SAMs 60Hz +SAM: contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; deltaf=60Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=5; + +$SAMs 250Hz +SAM: contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; deltaf=250Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=5; + +$SAMs 40% +SAM: contrast=40%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=40%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=40%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 20% +SAM: contrast=20%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=20%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=20%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 10% +SAM: contrast=10%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=10%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=10%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 5% +SAM: contrast=5%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=5%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=5%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 1% +SAM: contrast=1%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=1%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=1%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$SAMs 0.1% +SAM: contrast=0.1%; deltaf=(100..500..20,alternateout,r=3)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=2; +SAM: contrast=0.1%; deltaf=(20..90..10,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=1s; repeats=4; +SAM: contrast=0.1%; deltaf=(2..18..2,alternateout,r=2)Hz; am=false; freqsel=relative to EOD; duration=2s; repeats=4; + +$Chirps A +Chirps: chirpsize=120Hz; deltaf=60Hz; contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=250Hz; contrast=(40, 20, 10, 5, 2.5, 1, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, 0.005)%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false + +$Chirps f +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=20%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=10%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=5%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=1%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.5%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.1%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.05%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false +Chirps: chirpsize=120Hz; deltaf=(10,20,30,40,50,60,80,100,120,140,160,200,250,300,350,400,450,500)Hz; contrast=0.01%; chirpwidth=14ms; chirpampl=2%; repeats=16; am=false; sinewave=true; playback=false + +#$FICurve DC +#FICurve: am=false; + +#$Noise DC +#FileStimulus: file=/home/efish/stimuli/whitenoise/gwn150Hz10s0.3.dat; sigstdev=0.3; am=false; contrast=10% +#FileStimulus: file=/home/efish/stimuli/whitenoise/gwn150Hz10s0.3.dat; sigstdev=0.3; am=false; contrast=5% +#FileStimulus: file=/home/efish/stimuli/whitenoise/gwn150Hz10s0.3.dat; sigstdev=0.3; am=false; contrast=20% + + +############################################################################# +$AM +switch macrosam.cfg + +$Back +switch macros.cfg diff --git a/rfs/mirob2.t.zip b/rfs/mirob2.t.zip new file mode 100644 index 0000000..7db24d6 Binary files /dev/null and b/rfs/mirob2.t.zip differ diff --git a/rfs/relacs.cfg b/rfs/relacs.cfg new file mode 100644 index 0000000..568c6eb --- /dev/null +++ b/rfs/relacs.cfg @@ -0,0 +1,236 @@ +*Settings + Plugins: + pluginpathes : [ base*, calibration*, misc*, ephys*, efield*, efish*, comedi*, attcs3310* ] + pluginhelppathes: ~ + controlplugin : [ Session, Robot, AmplifierControl, SpectrumAnalyzer ] + modelplugin : PUnitModel + Pathes: + pathformat : %04Y-%02m-%02d-%a2a + defaultpath: dry/ + repropath : [ stimuli/repros/, reprodata, stimuli/repros/ ] + infofile : info.dat + Save: + saverelacsfiles : true + saveodmlfiles : false + savenixfiles : true + saverelacscore : true + saverelacsplugins: true + saverelacslog : true + saveattenuators : true + Date/time formats: + elapsedformat : "%02H:%02M" + sessiontimeformat: %Hh%02Mmin%02Ssec + reprotimeformat : %Mmin%02Ssec + Plotting: + printcommand: ~ + Data acquisition: + readinterval : 10ms + processinterval: 50ms + aitimeout : 10seconds + +*Metadata + -Setup-: + Identifier (Name): invivo1 + Maintainer : Jan Grewe + Creator : Jan Grewe and Jan Benda + Location (Room) : "5A17" + Lab : Neuroethology Lab + Institute : Institute for Neurobiology + University : University Tuebingen + Address : Auf der Morgenstelle 28 + +*RELACS + input data: + inputsamplerate : 20kHz + inputtracecapacity : 600s + inputunipolar : false + inputtraceid : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + inputtracescale : [ 100, 1, 10, 10, 100 ] + inputtraceunit : [ mV, mV, mV, mV, mV ] + inputtracedevice : [ ai-1, ai-1, ai-1, ai-1, ai-1 ] + inputtracechannel : [ 8, 0, 2, 4, 6 ] + inputtracereference: [ ground, ground, ground, ground, ground ] + inputtracemaxvalue : [ 200, 5, 3, 10, 10 ] + inputtracecenter : [ true, false, false, false, false ] + output data: + outputtraceid : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + outputtracedevice : [ ao-1, ao-1, ao-1, ao-1 ] + outputtracechannel : [ 1, 0, 2, 3 ] + outputtracescale : [ 1, 1, 1, 1 ] + outputtraceunit : [ V, V, V, V ] + outputtracemaxrate : [ 1kHz, 1kHz, 1kHz, 1kHz ] + outputtracemodality: [ electric, electric, electric, current ] + +*Macros + file : [ macrorfs.cfg, macros.cfg, macrosam.cfg, macrosdc.cfg ] + mainfile : macros.cfg + fallbackonreload: true + +*FilterDetectors + Filter1: + name : Spikes-1 + filter : DynamicSUSpikeDetector + inputtrace : V-1 + save : true + savemeanquality: true + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter2: + name : EOD + filter : EODDetector + inputtrace : EOD + save : true + savemeanquality: false + plot : true + trigger : true + buffersize : 300000 + storesize : true + storewidth : false + Filter3: + name : Chirps + filter : ChirpDetector + inputtrace : EOD + save : true + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : true + Filter4: + name : LocalEOD-1 + filter : EODDetector + inputtrace : LocalEOD-1 + save : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter5: + name : LocalBeat-1 + filter : BeatDetector + inputtrace : LocalEOD-1 + save : true + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + othertrace : Chirps + Filter6: + name : LocalEOD-2 + filter : EODDetector + inputtrace : LocalEOD-2 + save : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + Filter7: + name : GlobalEFieldStimulus + filter : EODDetector + inputtrace : GlobalEFieldStimulus + save : false + savemeanquality: false + plot : true + buffersize : 300000 + storesize : true + storewidth : false + +*AudioMonitor + device : [ "-1 default", "0 HDA Intel PCH: CX20642 Analog (hw:0,0) (2 channels)", "2 HDA Intel PCH: HDMI 0 (hw:0,3) (8 channels)", "3 HDA Intel PCH: HDMI 1 (hw:0,7) (8 channels)", "4 sysdefault (128 channels)", "5 front (2 channels)", "6 surround40 (2 channels)", "7 surround51 (2 channels)", "8 surround71 (2 channels)", "9 hdmi (8 channels)", "10 pulse (32 channels)", "11 dmix (2 channels)", "12 default (32 channels) - default" ] + enable : true + mute : false + gain : 1 + audiorate: [ "44.1", "8", "16", "22.05", "44.1", "48", "96" ]kHz + +*Devices + Device1: + plugin : AmplMode + device : dio-1 + ident : ampl-1 + buzzerpin : 14 + resistancepin: 15 + bridgepin : -1 + cclamppin : -1 + vclamppin : -1 + dclamppin : -1 + buzzerpulse : 500 + Device2: + plugin: [ Mirob, Mirob ] + device: dev + ident : robot-1 + Device3: + plugin: [ XYZRobot, XYZRobot ] + device: robot-1 + ident : robot-2 + +*Analog Input Devices + Device1: + plugin: ComediAnalogInput + device: /dev/comedi0 + ident : ai-1 + +*Analog Output Devices + Device1: + plugin: ComediAnalogOutput + device: /dev/comedi0 + ident : ao-1 + +*Digital I/O Devices + Device1: + plugin: ComediDigitalIO + device: /dev/comedi0 + ident : dio-1 + +*Attenuator Devices + Device1: + plugin: [ CS3310DIO, AttSim ] + device: dio-1 + ident : attdev-1 + Device2: + plugin : [ CS3310DIO, AttSim ] + device : dio-1 + ident : attdev-2 + cspin : 9 + mutepin : 10 + zcenpin : 11 + dataoutpin: 8 + datainpin : 12 + strobepin : 13 + +*Attenuator Interfaces + Device1: + plugin : LinearAttenuate + device : attdev-1 + line : 0 + aodevice : ao-1 + aochannel : 0 + ident : Attenuator-0 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + Device2: + plugin : LinearAttenuate + device : attdev-1 + line : 1 + aodevice : ao-1 + aochannel : 1 + ident : Attenuator-1 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + Device3: + plugin : LinearAttenuate + device : attdev-2 + line : 0 + aodevice : ao-1 + aochannel : 2 + ident : Attenuator-2 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + diff --git a/rfs/relacsplugins.cfg b/rfs/relacsplugins.cfg new file mode 100644 index 0000000..63f3b67 --- /dev/null +++ b/rfs/relacsplugins.cfg @@ -0,0 +1,752 @@ +*Metadata + Recording: + Recording quality: [ Fair, ~, good, poor, Poor, Fair, Good ] + Comment : "RF acoustically at 27, noise AM with LOCAL EOD, use 2nd baseline repro for baseline activity!" + Experimenter : [ Tim Hladnik, Tim Hladnik, MZ/TH, Martin Zeller, Dennis Huben, Janez Presern, Fabian Sinz, Juan Sehuanes, Carolin Sachgau, Jie Zhang, Jan Grewe, Jan Benda ] + WaterTemperature : 23.8°C + WaterConductivity: 330uS/cm + Cell: + CellType (Cell type) : [ P-unit, E-cell, E-cell deep, unknow, E-Cell, unkown, E-cell superficial, I-Cell, P-unit, Ampullary, T-unit ] + Structure (Recording location): [ Nerve, Nerve, Brain ] + BrainRegion : [ n.A., Torus, n.A., ELL ] + BrainSubRegion : [ ~, ~, LS, CLS, CMS, MS ] + Depth : 0um + Lateral position : 0mm + Transverse section : 0 + Subject: + Species : [ Apteronotus leptorhynchus, Apteronotus albifrons, Apteronotus leptorhynchus ] + Gender (Sex): [ unknown, unknown, Male, Female ] + Size : 13cm + Weight : 5.1g + Identifier : "2018lepto28" + -Preparation-: + Type : [ in vivo, in vivo, slice ] + Anaesthesia : true + Anaesthetic (Drug) : MS 222 + AnaestheticDose (Concentration): 100mg/l + LocalAnaesthesia : true + LocalAnaesthetic (Drug) : Lidocaine + Immobilization : true + ImmobilizationDrug (Drug) : Tubocurarin 5mg/L + ImmobilizationDose : 70ul + +*Control: Session + ephys: true + +*Control: Robot + General: + robot: robot-2 + Stored positions: + FishHeadPosition : "(362.162,407.166,223.354)" + FishTailPosition : "(362.162,277.865,250.954)" + MovementAreaStart : "(0,0,0)" + MovementAreaEnd : "(0,0,0)" + ForbiddenAreaStart: "(0.499,93.490,0.196)" + ForbiddenAreaEnd : "(340.000,447.802,253.921)" + CustomPosition : "(400.0,0.1,0.1)" + Tool clamp: + toolreleasedelay: 1s + toolfixdelay : 2.5s + autoclamp : true + +*Control: AmplifierControl + initmode : [ Bridge, Current-clamp, Dynamic-clamp, Voltage-clamp, Manual selection ] + resistancecurrent: 1nA + adjust : false + maxresistance : 100MOhm + buzzpulse : 500ms + showbridge : true + showcc : false + showdc : false + showvc : false + showmanual : false + syncpulse : 10us + syncmode : 0samples + +*Control: SpectrumAnalyzer + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + origin : [ before end of data, before signal, after signal ] + offset : 0ms + duration : 1000ms + resolution: 10Hz + overlap : true + window : [ Hanning, Bartlett, Blackman, Blackman-Harris, Hamming, Hanning, Parzen, Square, Welch ] + fmax : 500Hz + decibel : true + pmin : -50dB + +*Model: PUnitModel + General: + EOD: + eodtype : [ Apteronotus, None, Sine, Apteronotus, Eigenmannia ] + eodfreq : 800Hz + eodfreqsd : 10Hz + eodfreqtau : 10000s + eodlocalamplitude : 1mV/cm + eodglobalamplitude: 1mV/cm + localstimulusgain : 5.00 + globalstimulusgain: 0.00 + stimulusgain : 1.00 + Spikes: + voltagescale: 0.5 + Spike generator: + spikemodel: [ Wang-Buzsaki, Stimulus, Passive membrane, Morris-Lecar, Hodgkin-Huxley, Connor, Wang-Buzsaki ] + noised : 0.1 + deltat : 0.05ms + integrator: [ Euler, Midpoint, Runge-Kutta 4 ] + Voltage-gated current 1 - activation only: + gmc : 2 + emc : -90mV + mvmc : -35mV + mwmc : 10mV + taumc: 30ms + Voltage-gated current 2 - activation and inactivation: + gmhc : 0 + emhc : -90mV + mvmhc : -40mV + mwmhc : 10mV + taummhc: 10ms + pmmhc : 1 + hvmhc : -40mV + hwmhc : 10mV + tauhmhc: 10ms + pmhhc : 1 + +*Model: Stimulus + Input: + gain : 1 + offset: 0muA/cm^2 + +*Model: Passive membrane + Parameter: + R: 50MOhm + C: 25pF + Input: + gain : 1 + offset: 0muA/cm^2 + +*Model: Morris-Lecar + General: + params: [ Custom, Type I, Type II ] + Calcium current: + gca : 4nS + eca : 120mV + mvca: -1.2mV + mkca: 18mV + Potassium current: + gk : 8nS + ek : -84mV + mvk : 12mV + mkk : 17.4mV + mphik: 0.067kHz + Leak current: + gl: 2nS + el: -60mV + c : 20pF + Input: + timescale: 10 + gain : 1 + offset : 0muA/cm^2 + +*Model: Hodgkin-Huxley + Sodium current: + gna: 120mS/cm^2 + ena: 50mV + Potassium current: + gk: 36mS/cm^2 + ek: -77mV + Leak current: + gl : 0.3mS/cm^2 + el : -54.4mV + c : 1muF/cm^2 + phi: 1 + Input: + gain : 50 + offset: 10muA/cm^2 + +*Model: Connor + Sodium current: + gna: 120mS/cm^2 + ena: 50mV + Potassium current: + gk: 20mS/cm^2 + ek: -77mV + A current: + gka: 47mS/cm^2 + eka: -80mV + Leak current: + gl : 0.3mS/cm^2 + el : -22mV + c : 1muF/cm^2 + phi: 1 + Input: + gain : 50 + offset: 30muA/cm^2 + +*Model: Wang-Buzsaki + Sodium current: + gna: 35mS/cm^2 + ena: 55mV + Potassium current: + gk: 9mS/cm^2 + ek: -90mV + Leak current: + gl : 0.1mS/cm^2 + el : -65mV + c : 1muF/cm^2 + phi: 5 + Input: + gain : 50 + offset: 6muA/cm^2 + +*Event Detector: Spikes-1 + Detector: + minthresh: 23.0mV + ratio : 15% + testwidth: false + fitwidth : 3.00ms + +*Event Detector: EOD + threshold : 0.44mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: Chirps + minthresh: 10Hz + +*Event Detector: LocalEOD-1 + threshold : 1mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: LocalBeat-1 + minthresh: 0.050mV + ratio : 35% + +*Event Detector: LocalEOD-2 + threshold : 1mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*Event Detector: GlobalEFieldStimulus + threshold : 0.052837mV + interpolation: [ linear interpolation, closest datapoint, linear interpolation, linear fit, quadratic fit ] + +*RePro: Pause + duration : 0sec + savedata : false + plotwidth: 0sec + +*RePro: Record + duration : 1sec + plotwidth: 0sec + dioout : false + diodevice: dio-1 + dioline : 0 + +*RePro: SaveTraces + General: + duration : 1sec + savedata : false + split : false + dioout : false + diodevice: dio-1 + dioline : 0 + Analog input traces: + trace-V-1 : true + trace-EOD : true + trace-LocalEOD-1 : true + trace-LocalEOD-2 : true + trace-GlobalEFieldStimulus: true + Events: + events-Spikes-1 : true + events-EOD : true + events-Chirps : true + events-LocalEOD-1 : true + events-LocalBeat-1-1 : true + events-LocalBeat-1-2 : true + events-LocalEOD-2 : true + events-GlobalEFieldStimulus: true + +*RePro: SetAttenuatorGain + outrace : V-1 + gain : 1 + interactive: true + +*RePro: SetInputGain + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + gainindex : 3 + interactive: true + +*RePro: SetOutput + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + value : 0V + intensity : 1 + interactive: false + +*RePro: Spectrogram + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + width : 100ms + step : 0ms + tmax : 10s + duration: 0s + size : [ "1024", "64", "128", "256", "512", "1024", "2048", "4096", "8192", "16384", "32768", "65536", "131072", "262144", "524288", "1048576" ] + overlap : true + window : [ Hanning, Bartlett, Blackman, Blackman-Harris, Hamming, Hanning, Parzen, Square, Welch ] + powermax: true + fmax : 2000Hz + pmax : 0dB + pmin : -50dB + +*RePro: TransferFunction + Stimulus: + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + offsetbase: [ custom, current ]value + offset : 0V + amplitude : 1V + clip : 4 + intensity : 1 + fmin : 0Hz + fmax : 1000Hz + duration : 1s + pause : 1s + repeats : 100 + Analysis: + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + size : [ "1024", "64", "128", "256", "512", "1024", "2048", "4096", "8192", "16384", "32768", "65536", "131072", "262144", "524288", "1048576" ] + overlap : true + window : [ Hanning, Bartlett, Blackman, Blackman-Harris, Hamming, Hanning, Parzen, Square, Welch ] + plotstdevs : true + plotcoherence: true + plotdecibel : false + +*RePro: Wait + absdate: false + date : ~ + days : 0days + time : "00:00:00.000" + +*RePro: AttenuatorCheck + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration : 1s + type : [ attenuation, noise ] + frequency: 50Hz + amplitude: 1Vmax + minlevel : 0dB + maxlevel : 100dB + dlevel : 1dB + adjust : true + +*RePro: InputRangeCheck + outtrace: [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration: 1000ms + pause : 1000ms + amplnum : 10 + +*RePro: RestartDelay + duration: 100ms + repeats : 100 + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + +*RePro: StimulusDelay + intrace : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + outtrace : [ GlobalEField, GlobalEFieldAM, LocalEField, I ] + samplerate: 10kHz + duration : 10ms + pause : 50ms + repeats : 100 + setdelay : [ none, minimum, mean ] + +*RePro: BridgeTest + amplitude : 1V + duration : 10ms + pause : 100ms + average : 10 + skipspikes : true + dynamicrange: false + rate : 0.01 + plottrace : true + +*RePro: CalibrateSyncPulse + imin : -1 + imax : 1 + istep : 0.001 + skipwin : 1000ms + duration: 1000ms + +*RePro: CapacityCompensation + amplitude : 1V + duration : 200ms + frequency : 100Hz + showcycles : 10 + pause : 100ms + average : 10 + skipspikes : true + dynamicrange: false + rate : 0.01 + +*RePro: Iontophoresis + durationpos : 1s + amplitudepos : 1V + pausepos : 1s + durationneg : 1s + amplitudeneg : 1V + pauseneg : 1s + fortunes : true + fortuneperiod: 10s + +*RePro: SetLeak + interactive : true + preset : [ previous, zero, custom ]values + g : 0nS + E : 0mV + reversaltorest: true + involtage : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration : 100ms + +*RePro: SetVGate + interactive : true + preset : [ previous, zero, custom ]values + g : 0nS + E : 0mV + vmid : 0mV + width : 0mV + tau : 10ms + reversaltorest: true + involtage : [ V-1, EOD, LocalEOD-1, LocalEOD-2, GlobalEFieldStimulus ] + duration : 100ms + +*RePro: Beats + Stimulation: + duration : 10seconds + pause : 20seconds + ramp : 0.5seconds + deltafrange : "10"Hz + deltafshuffle: [ Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + fixeddf : false + amplitude : 1mV/cm + amtype : [ none, sine, rectangular ] + amfreq : "1"Hz + amamplitude : "100"% + repeats : 10 + fakefish : 0Hz + Chirps: + generatechirps : false + chirpsize : 100Hz + chirpwidth : 100ms + chirpampl : 0% + chirpkurtosis : 1 + chirpfrequencies: ~Hz + chirptimesfile : ~ + chirptimeshuffle: [ Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + Analysis: + before : 1seconds + after : 1seconds + averagetime : 1seconds + usepsd : true + mineodfreq : 100Hz + maxeodfreq : 2000Hz + eodfreqprec : 1Hz + neod : 2 + showstimulus: false + split : false + savetraces : false + +*RePro: CalibEField + General: + reset : true + resetval : 0.1 + am : false + beatfreq : 10Hz + frequency: 670Hz + duration : 600ms + pause : 10ms + Range: + amplsel : [ contrast, amplitude ] + targetcontrast : 25% + mincontrast : 25% + maxcontrast : 65% + targetamplitude: 1mV/cm + minamplitude : 0.5mV/cm + maxamplitude : 2mV/cm + numintensities : 10 + +*RePro: CalibrateRobot + robot: robot-2 + +*RePro: EFieldGeometry + Enviroment data: + temperature : 26°C + conductivity: 330µS + water_level : 20cm + Measurement data: + robot : robot-2 + type : ~ + distance : 0mm + head_length : 20mm + tail_length : 20mm + width_posY : 50mm + width_negY : 50mm + height : 50mm + depth : 50mm + step_length_x: 5mm + step_length_y: 5mm + step_length_z: 5mm + +*RePro: JAR + Stimulation: + duration : 10seconds + pause : 10seconds + ramp : 0.5seconds + deltafstep : 2Hz + deltafmax : 12Hz + deltafmin : -12Hz + deltafrange : ~ + deltafshuffle: [ Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + repeats : 200 + Amplitudes: + amplsel : [ contrast, absolute ] + contrastmax : 20% + contrastmin : 10% + contraststep: 20% + amplmin : 1mV/cm + amplmax : 2mV/cm + amplstep : 1mV/cm + S&timulus: + genstim : true + sinewave: true + file : ~ + sigstdev: 1 + warpfile: false + fakefish: 0Hz + A&nalysis: + before : 1seconds + after : 8seconds + savetraces : true + jaraverage : 500ms + chirpaverage: 20ms + eodsavetime : 1000ms + +*RePro: LinearField + duration: 1s + +*RePro: ManualJAR + deltaf : 0.0Hz + lineardeltaf : false + deltaf2 : 0.0Hz + amplitude : 1.0mV + duration : 10seconds + ramp : 0.5seconds + fakefish : 0Hz + showlineardeltaf: false + before : 1seconds + after : 1seconds + averagetime : 1seconds + split : false + savetraces : false + +*RePro: BaselineActivity + Timing: + duration: 300ms + repeats : 0 + Analysis: + isimax : 20ms + isistep : 0.2ms + ratedt : 0.05ms + ratetmax: 2ms + Files: + eodduration : 2000ms + saveeodtrace: false + saveeodtimes: false + Control: + auto : [ never, once, always ] + adjust: false + +*RePro: Chirps + Chirp parameter: + nchirps : 10 + beatpos : 10 + beatstart : 0.25 + minspace : 200ms + firstspace : 200ms + chirpsize : 100Hz + chirpwidth : 14ms + chirpampl : 2% + chirpsel : [ generated, from file ] + chirpkurtosis: 1 + file : ~ + Beat parameter: + deltaf : 10Hz + contrast: 20% + am : false + sinewave: true + playback: false + pause : 1000ms + repeats : 6 + Analysis: + sigma : 2ms + adjust: true + +*RePro: FICurve + Test-Intensities: + duration : 400ms + maxintfac : 180% + minintfac : 20% + nints : 16 + repeats : 1 + blockrepeats : 10 + singlerepeats: 1 + intshuffle : [ AlternateOutUp, Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + intincrement : -2 + Pre-Intensities: + preduration : 0ms + maxpreintfac : 140% + minpreintfac : 60% + npreints : 2 + preintshuffle: [ AlternateInDown, Up, Down, AlternateInUp, AlternateInDown, AlternateOutUp, AlternateOutDown, Random, PseudoRandom ] + Control: + am : true + pause : 1000ms + delay : 200ms + onsettime : 50ms + rangeintincrement: 4 + minrate : 40Hz + minratefrac : 15% + adjust : false + +*RePro: FileStimulus + Stimulus: + file : /home/efish/stimuli/whitenoise/gwn300Hz10s0.3.dat + sigstdev : 0.3 + duration : 0ms + pause : 1000ms + amplsel : [ contrast, absolute ] + contrast : 20% + amplitude: 1mV/cm + am : true + repeats : 10 + Additional noise: + noisetype : [ none, Gaussian-White, Ornstein-Uhlenbeck ] + uppercutoff : 300Hz + lowercutoff : 0Hz + noisetau : 100ms + noisecontrast: 5% + noiseampl : 80mV/cm + Analysis: + binwidth: 5ms + before : 0ms + after : 0ms + plotpsd : false + psdsize : [ "256", "64", "128", "256", "512", "1024", "2048", "4096", "8192", "16384", "32768", "65536", "131072", "262144", "524288", "1048576" ] + adjust : false + +*RePro: ReceptiveField + Quick Search: + xmin : 27mm + xmax : 128mm + xstep : 5mm + ymin : 0mm + ymax : 0mm + ystep : 1mm + ystart : 0mm + zmin : -20mm + zmax : -20mm + zstep : 1mm + followmidline: true + Stimulation: + deltaf : 20Hz + amplitude: 10mV + duration : 1000ms + pause : 250ms + repeats : 4 + binwidth : 20ms + Robot setup: + xmapping: [ y, z, x ] + xinvert : true + ymapping: [ z, x, y ] + yinvert : true + zmapping: [ x, y, z ] + zinvert : false + safex : 410mm + safey : 315mm + safez : 205mm + +*RePro: RobotToFishPosition + Position: + destination : "(27,0,-20)" + followmidline: true + Robot setup: + xmapping: [ y, z, x ] + xinvert : true + ymapping: [ z, x, y ] + yinvert : true + zmapping: [ x, y, z ] + zinvert : false + +*RePro: SAM + Stimulus: + duration : 1000ms + pause : 1000ms + freqsel : [ relative to EOD, absolute ] + deltaf : 20Hz + contrast : 20% + repeats : 6 + am : true + sinewave : true + ampl : "0.0" + phase : "0.0"pi + contrastsel: [ fundamental, peak amplitude ] + Analysis: + skip : 0.5Periods + ratebins: 10 + before : 0ms + after : 0ms + adjust : false + +*Attenuator-0 + plugin : LinearAttenuate + ident : Attenuator-0 + device : attdev-1 + line : 0 + aodevice : ao-1 + aochannel : 0 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + frequencyname : ~ + frequencyunit : Hz + frequencyformat: %7.0f + gain : 0.43737 + offset : 0 + +*Attenuator-1 + plugin : LinearAttenuate + ident : Attenuator-1 + device : attdev-1 + line : 1 + aodevice : ao-1 + aochannel : 1 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + frequencyname : ~ + frequencyunit : Hz + frequencyformat: %7.0f + gain : 0.045983 + offset : 0 + +*Attenuator-2 + plugin : LinearAttenuate + ident : Attenuator-2 + device : attdev-2 + line : 0 + aodevice : ao-1 + aochannel : 2 + intensityname : amplitude + intensityunit : mV/cm + intensityformat: %6.3f + frequencyname : ~ + frequencyunit : Hz + frequencyformat: %7.0f + gain : 1 + offset : 0 +